Traumatizing Tray?

When we can't be with our puppy we crate him. A few days ago, my sister swept out the fur in the plastic tray in the crate. It's a wire crate so the tray can slide in and out. She forgot to lock the tray into the crate. Yesterday I came downstairs to let Tyson out and I found that half of the tray had slid out of the crate and Tyson whimpering. He looked scared and was pushed near the crate door standing on what little bit of the tray was still inside of the crate. I immediately let him out and took him outside to pee. Then brought him back inside where I pushed the tray in and locked it in. I've started to notice now that whenever I crate him, he'll bark and howl after we put him in. Before he was very good with the crate. He didn't necessarily walk in on his own but he didn't mind the crate after we trained him. He's crated at night(not in my room since my parents don't want him upstairs in the bedrooms) and during the day when we have to go out. I always take him out to pee/poop before I put him in his crate so when he barks and howls right after I put him in I don't let him out or it'll just encourage his noisemaking. I'm worried now that he's traumatized because the tray slid out from underneath him. Is that possible? And if so, how can I make him comfortable with his crate again? Or is this something that he'll probably just forget with time and not be scared anymore?